I'm interesting in converting one or more of my existing modules for Dungeons and Dragons 3/3.5e to work with the Pathfinder rules. I'm interested to know from others who have done this kind of conversion what difficulties they ran into and what things I should keep in mind and watch out for in order to make that conversion a success.

For example, how have you handled converting an NPC's or monster's stats (for those monsters that don't have specific Pathfinder equivalents) to make them the equivalent strength and "CR" under the new rules? It would seem to me that in these cases, when character classes have been strengthened a bit, that to keep things even you would need to strengthen your NPCs or monsters or they would be a weaker battle.

2 Answers
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I have been running a Pathfinder campaign for two years and have used plenty of 3e and 3.5e adventures in it as well as native Pathfinder ones. (I've used multiple adventures from the Atlas Games Penumbra series, Green Ronin Freeport series, Goodman Games Wicked Fantasy Factory series, and older Paizo 3.5e APs and Pathfinder Modules.)

The short form is that 3e monsters/encounters count as CR (or EL)-2, and 3.5e ones count as CR (or EL)-1. In other words, you need a CR 8 3e monster or NPC to provide the punch a CR 6 one does in Pathfinder.

Besides that, you can do as much conversion as you want, but you really don't have to do any. Just run adventures higher in the range band - "D&D 3e for levels 3-5" means use on level 3 characters max unless you want to do conversion work.

My general process when using old ed adventures and actually converting is:

Convert major NPCs. This is where you get the largest differential, and you want your "bosses" to shine; it's not just hit points and attack bonuses but the cool new feats and classes and whatnot you want them to benefit from. I usually use Hero Lab to do NPC builds. (Many of the 3.5e Paizo APs have had fan conversions to Pathfinder posted on the Paizo forums.) My level 4 PCs can dogpile the heck out of a level 8 NPC boss if they're not done up well.

Sub in monsters where they exist in PF. Simple. Just look them up in the Bestiary(/2/3) and use those stats instead.

For lesser NPCs and monsters, either use tougher ones, more of them, or give them a quickie advanced template (or heck, just boost their hit points). For lesser NPCs, if you have the NPC Guide or Gamemastery Guide, there are a bunch of great NPC builds of various levels you can use for normal guards/bandits/soldiers/pirates/townsfolk/etc. and reskin as needed.

And that's it! I don't have the patience to do more, and unless you're publishing it there's no reason to.

Keep in mind that spellcasters get their 0th level spells at will in Pathfinder. This makes it perfectly reasonable to cast detect magic on everything and possibly identify it, makes prestidigitation and mage hand useful, and so on. Nothing scenario-breaking, but something that you should be aware of.